Journal of The Forgotten-
by starfreak23
Summary: There's one thing that the Doctor can't remember. He can't explain why, or how he can remember everything around that he forgot, except her. Who is she? Serenity Reynolds is the forgotten companion. Takes place between the War Doctor and Rose. First Who-Fic! Please R&R!
1. Prologue

**A/N**: Hello, my lovelies! Long time no write! I know I should be continuing other things but I'm sort concentrating on grades so I've been keeping myself off writing a bit... BUT, I had a plot bunny jump into my head and I couldn't chase the damned thing away before it started to multiply so I'm posting the prologue now! My first Who-fic, so please keep that in mind, but otherwise, Enjoy!

"S, S, S, S..." The Doctor called as he dug through the trunk he kept as his attic, so to speak.

Clara Oswin Oswald stood behind him, arms crossed over her chest as she looked upon him curiously as she compared her travel partner to a certain British nanny from the early 20th century.

"Doctor, what are you looking for?"

The man paused and looked up, his flap of hair bouncing a hit with the force of his movement. "Truth be told, Clara, I don't know. Something Interesting. Something to do, something to show you." He responded excitedly as he went digging in his amazing magic trunk once more disappearing into it from the waist up. "Sash of Rassilon, my security disk, my skinsuit, ooh that belonged to the Slitheen, and-" He suddenly paused, sounding as if something had suddenly stolen his voice and he hadn't noticed.

"Doctor? Are you alright?" His companion asked, reaching out to touch his side, almost as if to prove his now still body alive.

He slowly slid back up and sat on his ankles, a small leather bound journal held loosely in his hands. The engraving on the cover was on a group of Stars, the initials S.R. a constellation in a brown galaxy, though it seemed the lines connecting them had been carved in as an afterthought, or maybe even added on by request, not as up to par with the rest of the carving. The leather was worn by the natural oils of human skin, but also from time and use, as if the person, this S.R., had written in it every night, or had never let it out of their sight.

"For all my lives, I can never remember this until I stumble upon it again."

The words jarred something in Clara that she initially did not like. "Like the silence? You can't remember it until you look at it again?" Large brown eyes flooded with worry as she kneeled with him, slowly reaching for the book as though she meant to dispose of it.

The time lord chuckled and shook his head. "Nice try, Clara, but no. I just seem to forget, it fades from my memory after a while and I can never tell why. I never forget something."

His reassurance calmed her a bit, but she grabbed it from him anyways, softly turning it in her hands as if she expected it to disintegrate into a pile of dust from age is she handled it wrong. An egg for her to inspect. "What is it?"

"That is quite obviously a diary of some sorts, Clara, do use your head." He playfully condescended, allowing her to glare with a similar humor at him.

He grabbed it back, considerably less careful with it than she was as he popped up, running down a corridor for her to clumsily follow. "Doctor, where are you going?" She shouted as she caught up to him, watching him skid into the library and stop, breathing in the familiar scent of books.

"It's a book, I thought we should read it in the library. The comfy chairs are in here, anyways." He spurted as he grabbed her by the wrist and led her to a small section with a coffee table and a living room set up, the sitting objects plush and quite comfy, as he had said.

Clara followed diligently, curious as to why he was willing to slow down and show her something as simple as a diary. She concluded that the author must have been an extremely important person as he settled on a couch patting the seat next to him with one hand as he pulled his glasses out of relatively nowhere, the book settled on his lap.

She sat and cuddled up to him as he finally lifted the book, earning her an awkward look from him. "What? I have to be close to read the book and it's comfortable!" She defended, earning another, more skeptical look before he placed an arm around her gingerly and held the book with both hands.

He took a breath to speak when Clara interrupted. "So the book was probably written by someone really important, yeah? Like, a great leader?"

"I don't know Clara, let's read and find out."

"I mean, it's gotta be pretty important for you of all people to just sit down and read because you're a pretty jumpy person." He took another breath to respond. "But, you know what-"

"Clara," he nearly snapped, sounding a bit exasperated. "I know that I've read this book over a hundred times, but I can never remember what's in it. I might as well read it with someone who might remember what I think needs to be remembered."

"How do you...?" She trailed off, knowing he wanted her to shut up so that they could read.

"I may be a bit of a pack rat, but I wouldn't have kept something like this unless it had some significance. At least, not in there."

She nodded in understanding and nuzzled up to him as he slowly began to read the contents of the story aloud.

**A/N: **Okay, I know that was short for me, but it's a prologue, give me a break! The first chapter should come up while I'm on spring break If things go as planned, but don't get your hopes very high, I would hate for you to be disappointed. NOTE! The entire story will not be written as them reading, so keep on reading this and find out who this S.R is, and why can't the Doctor, of all people remember?


	2. The Caged Girl Meets the Madman

**A/N: **Okay, but I lied. When I said the next chapter should be up during spring break? I should have said the one after THIS one. I had most of this one written already, so I just finished it today as a gift to all of you lovely readers! I hope you like what I wrote… Again, some stupid rabbit I couldn't chance away began to multiply. Tell me what you think!

**Disclaimer**: I don't own Who, Monsters Inc., or the U.S. Military, though it'd be pretty cool for any of them to be mine.

_Shouting... so much shouting. A ruined braid now ran down her back, but the space where it had been tucked under the rest of her hair was raised enough so that the largest of the three men had been able to get a grip on the back of her head and force her into the tank of freezing, dirty, black water she was now slowly drowning in. The smallest held her arms to her back, almost breaking them with his surprising strength as the third had her legs raised off of the floor. Struggling had been proven futile when her strength had deserted her, a while back, her breathing pattern now holding her priority. Any movement drove her deeper into the water, the laughter above her muffled, yet burrowing into her ears as the stuff of nightmares. Pain webbed out in her chest as the oxygen level lowered like the visibility range of her tunneled vision. _

_Someone from behind her shouted as she was wrenched from the water, gasping in relief and unable to even whimper out of pain. _

_Even more shouting, unintelligible words echoing through the walls of the dank cave surrounding them, tears leaking out of her eyes sliding silently down her cheeks. _

The young soldier had practice in waking up, terrified, yet silent, from her nightmares. Even the smallest sign of terror would have gotten her beaten, though her captors didn't seem to need an excuse. "Come on, Serenity, there's nothing you can do." Sitting up, she struggled to avoid the barbed wire of the 'Sally Port' she was held in, shivering and struggling to remember just how long it had been. Her lieutenant's pin was discarded into the corner of the floor, the cage only extending seven feet by six feet, useless other than to scratch lines into the floor. "How many is that, now? What am I even counting? The days? The nightmares?"

_Does it even matter anymore?_

Serenity winced as a voice shouted at her to shut up in a language she could only assume to translate. God only knew exactly how long it had been since her convoy had been ambushed, since she had been dragged from the wreckage of an IED induced blast and hauled off to this hole in the middle of a barren desert.

She laid back and closed her eyes, listening to the sounds around her and struggling to ignore the age old pain shooting up her back from straightening after so much time bent out of shape. Pain was almost a dull numbness in the back of her mind, now, after so much exposure to something, one developed an immunity, but her clenched jaw seemed proof that no immunity is final.

Footsteps were a common sound on the outside of the starving soldier's cell, the sound of men running with weapons was not a rare sound either, though the spark of hope that grew when hearing it had merely turned into a smoldering ember in the dying fire that was the young lieutenant's heart. There was a constant dripping noise, too, water from some underground stream that slowly dripped down one of the few short stalactites. The pattern, over time, had morphed into several different songs, keeping her amused as she softly sung to whichever beat the droplets chose to lay that night until sleep overtook her in its grip. A choke hold, broken only by nightmares of torture... Or torture itself.

A new branch of an even more familiar pain sprouted from her as her stomach, starved of nutrients for days at a time, decided it would wait no longer. A low rumble was hidden by a soft groan of agony from the woman in the small cell, also hiding from her the fact that a set of feet had stopped outside of the bulkhead door of the room her cell was in.

"Hello?" Was the word that silenced her, a fear of man being discovered in hearing her native tongue of English, amplified irrationally by the sound of it not in a familiar American accent. "Is there anyone in there?"

_You're hallucinating out of pain, Reynolds. Hold yourself together. Pain is weakness leaving the body... But, we are oh so weak._

She could feel old wounds being agitated by her body curling up in a ball, new ones forming from barbed wires what now dug into exposed flesh on her back at the exact same action, the all too familiar watery sensation of dripping blood spawning. Another, louder, pained whimper escaped her throat, in which the man on the other side of the door obviously heard.

A machine began whizzing from his side, a high frequency whine filling the air and stabbing at wounded ears like a precisely positioned scalpel caused a choked scream to escape sandpaper lips. A pair of terrified blue eyes shot open.

"I swear, I'll get you out of there, I can help. I'm the Doctor-" His words were interrupted by the screeching of rusted metal hinges as the thick metal door slowly creaked open to allow just enough light from the flickering lamp in the corridor to cast a shadow in her direct line of sight. Lieutenant Reynolds shut her eyes in terror once more.

The man ran into the room, an almost growl emanating from his throat as he stepped to the door at her feet.

_I showed a weakness... They're coming to get me for another round... Maybe this time they'll finally let me die. Maybe this time, it'll finally end._

_"_Humanity. This is what you do to each other, now, is it?" The whine was back as his voice slowly rose in anger. "Find a way to capture one of your own and lock her in a cage like an animal. A toy for anyone's sadistic pleasures." The door was opened more gently this time, contrary to the emotion in his thickly accented voice, an accent that the beaten woman was too drained to even attempt to translate.

Her eyes shot open as a gentle hand brushed a strand of grimy brown hair behind her ear, meeting a similar pair of eyes, only pained in a different way, terrified themselves instead of malicious as she had grown accustomed. "Pl-please..." She pleaded, finally realizing how sandpaper like her once melodic voice had become. "Let me die."

His eyes were sad, as if they had seen so much more than they seemed, but they were kind as well. Empathetic. The rest of his face in a blur, an overly wet water color painting dripping color down the sides, a vague shape, visible but beautifully smudged except for her one area of focus. The one thing that she thought, perhaps reflected exactly her own eyes, perhaps not a man at all, but a mirror to torture her further. But the words that escaped his lips next never reached her ears, and she didn't need them to.

Because, the disagreeing shake of his head, she decided, had been the cruelest thing of all the tortures they had delighted in. Her last sight before the tentacle like fingers of pain braided around her mind and led her into unconsciousness.

This time, Serenity Reynolds screamed when she woke, writhing and thrashing, trying to get away from the men who had beaten her, who had come so close to using her for themselves, who had branded the word fear into her subconscious and laughed, towards the kind set of eyes that she had last seen before the pain had become too much.

_You're not in the cell_

Her eyes shot open further and she could see nothing but golden sparkles floating around her as if a Star Trek style teleporter mid-transport. Her body, suspended in the air somehow, not touching any surface and not allowing her to move any more than a strained wriggle. Which, scared her even more. "H-he-hello?"

The walls were stark white, but with a low light so that they seemed in a more comfortable environment; the smell of what used to be a completely sterile room sullied by the smell of blood and sweat. A noise of some sort of engine, whirring in a soft, deep thrum below her, throwing her off from her guess that she could be in an airplane of some sorts, and she knew she was not in a hospital.

_You're dead. The angel of death carried you home and they let you di-_

"Oh, bloody marvelous." A voice muttered, though there was no true malice behind it and the eyes returned. He approached and took her hand, his touch firm but more gentle than she had felt in too long. "It's okay, you're safe now. I'm the Doctor, and I promise nothing is going to hurt you."

The corner of her chapped lips quirked upwards as she nodded. More of the man's face was visible, even in the low light, pale skin shone a shade of almost alabaster as he stepped into the golden sheen of the transporter-sparkle-things, the crinkle of crow's feet hinted how much he liked to smile, but the eyes themselves still worried as he scanned a colorful screen above her chest, roughly tapping out responses to the computer's readouts, a heartbeat monitor slowly coming online.

Their eyes met once again as he hesitantly reached down and curled his fingers around her lightly shaking digits in a kind comfort. "Sleep now, sweetheart, there will be no more nightmares tonight. And, you damned sure deserve it after what you've been through."

Pained ears finally listened to her command as sleep gently overtook her and eased her into a dreamless unconsciousness.

For once, there was no pain as the lieutenant opened her eyes once more to the strange interior of what she assumed was an advanced hospital. The mattress she laid on curved perfectly into her back and she felt as though she had actually eaten in less than 8 hours, a soft cotton blanket the only thing shielding her body to the brisk air that stroked her face in a gentle current.

_I'm on a mattress... a mattress, not the floor! Ha! _

She couldn't feel an IV unit in her arm, nor could she hear or see any machines that may have belonged in a hospital, which worried her slightly. Serenity sat up, stiffly using her arm to keep the blanket in place as she surveyed the room.

It seemed to be a post-op room, from what she had seen in the few hospitals she had the displeasure of being in, and yet it was nothing like it. The room was dimmer, but was gradually getting brighter as though linked to her state of awareness. A futon-looking couch stood at the wall near the foot of her bed, along with a chair to her left side with an indent as though someone had sat there recently. Her tattered uniform was nowhere to be seen, but a melodic tenor wafted from the door to her right, footsteps increasing in volume as the humming did.

The man who entered was the man she had seen as her angel, kind eyes smiling at her as he carried a tray of food to her place on the clean sheeted mattress. "Good, you're awake." The smile in his eyes slid down to his thin lips as he beamed at her, teeth showing and everything, the kindest look anyone had given her in what felt like years. "How are you feeling?"

This time it was easier for the young lieutenant to speak now, more of the song-like cadence that was once always present in her voice had returned, though it sounded more of a lamentful song, now, a song that told of past pain and fear, though she still smiled politely. "I'm feeling much better now, sir, thank you. This is better living accommodations that I've seen since- well, for a long time." A soft chuckle reverberated from her throat as she tightened her smile in humor.

The man, who had now sat next to her on the chair, having set the food across her waist and assisted her to sit up enough to eat, chuckled himself. The plate consisted of a thick white soup with chunks of pale vegetable floating around in it, a small glass of water and a vase with a single peach peony inside as if to cheer up the meal a bit more. "It's New England clam chowder, by the way. Your uniform had an American flag so I assumed you'd know the dish. And, don't 'Sir' me, I'm the Doctor." There was a humorous tone to the turning down of the respectful term, and she could finally get a good look at the man.

Thinning brown hair on his head led to the soft crinkles of his forehead, even more prominent when he raised his eyebrows as he spoke, dark eyelashes framed the same kind, sea glass blue eyes that had greeted her before. His lips were thin, but seemed to have an upwards quirk to them more often than not, a pale mole adorning the far side of his right cheek. "Doctor what?"

At this, he seemed to furrow his eyebrows. "Excuse me?"

Serenity blushed a bit, raising the spoon and beginning to pick at the soup in her bowl, still using the insides of her arm to keep the blanket up. "I don't mean to be rude, but I was asking your last name. Doctor what?"

He seemed to take her words to ponder for a bit, before raising his head from it's slightly down tilted position. "That's a different way of asking it. Nothing, just the Doctor. Now, eat before it gets cold and before you starve." He picked up the spoon from where she had set it down and turned it so that she could grab the handle, the left corner of his mouth quirking up in a kind smile.

The soldier took it eagerly, nodding in a silent thank you, before she began to all but inhale the food he had set in front of her. And that is when the questions began.

"Who are you?"

"Major Serenity Reynolds of the US army. 56-542-398." She answered simply, her training kicking in and electing the correct response as if it were an interrogation.

"Bollocks, your uniform had a Lieutenant's stripes, so now that you're confused as to who you are, I can tell you're either lying, or trying to make yourself sound important." He grinned as he spotted her mistake as soon as it came out of her mouth. She glared into her food and muttered back to him.

"The latter. I'm a lieutenant."

"Why were you there, Lt. Reynolds?"

"I'm just a supply officer, so I have no idea why they would choose me as a bargaining chip. We were going to deliver to a base in Saudi Arabia, I hadn't heard exactly where we were going yet but I think it was Camp Commando, and suddenly, in the middle of the desert we're all but being showered in IEDs and-" The soldier was now reliving the moment behind her eyes, shaking hands clutching at her sides as she relived her frustrations. "By the time I had my pistol out someone had knocked me to the ground and out. I woke up in a cave-" The doctor rested his hand upon Serenity and she slowly drew herself out of it. "And the rest is a bit obvious."

"How in the 'Verse did you make it halfway into Iraq then?" He mumbled quietly, though her exclamation was cut short by his sudden question. "Where are you from, Serenity?" He used her first name and it got her to smile a bit as she met his eyes.

"Garden City, Georgia, sir- Doctor." The soldier stumbled, so used to having to address people in a certain way that she even made herself giggle. "Where are you from, If I may ask?"

"Where do you think I'm from?"

Two pairs of steely blue eyes met, and she glared playfully. "Doc, I'm an American. You could have been my neighbor as a kid and I never even knew."

The man in the jumper chuckled and leaned a bit back. "You wouldn't believe me if I told you."

"Try me."

"Gallifrey."

"Where?"

He stood and chuckled, almost sadly as he began to clear the tray off and place it on a nearby table she hadn't seen before. "Not on Earth, I can tell you that much. I'm not human. Don't give me that look, I can prove it."

_Okay, now I'm starting to think I'm having some weird ass dream. My 'Angel' is now a self-proclaimed Alien. _

The patient blushed a bit when she realized she had been wearing her emotions on her face and mumbled a short apology before asking the simple question. "How?"

"I have two hearts."

_Yup. I'm going nuts_

"Okay, then..." She trailed off, causing her angel to chuckle and press a few buttons on the monitor above her, the one that had been above her chests the last time she had woken up. The gilded sparkled formed again, this time creating a diagram of his chest in the air above her, almost as if it were a live action feed as the organs, including two hearts, moved in accordance to his breathing and movements Reaching out to touch it, she found that they shied from her touch, being what snapped her out of her A.D.D trance, allowing her the chance to shoot him an amused glare. "Doc, we are in the year 2013, the technology to do make holograms is not that farfetched, and actually, it already exists. You're going to have to do a bit better than that."

The self-proclaimed alien narrowed his eyes, always ready to accept a challenge. "This is what happens when you don't start with the T.A.R.D.I.S..." He mumbled to himself, willing the shimmers to disappear. "Those, my young leftenant, were Nanogenes, not a hologram. Those, are what healed you, and without those, you would be dead." His tone was almost dismissive, as if he wasn't actually thinking of the consequences behind the nanogenes having not existed. "I'll be able to prove it when you are well enough to walk."

"I can walk..." She mumbled, not meeting his eyes which obviously challenged the remark. Before she could justify why it bugged her so much, she was wrapped tightly in her sheet and attempting to stand on her own, failing miserably.

He flew across the room to wrap his arms around her and steady her, allowing her to stand with his weight as her support. He eyed the cloth that barely sheathed her from the cold and murmured. "Let's get you some real clothes, yeah?"

Serenity chuckled and nodded, wrapping the sheet a bit tighter as she steadied herself. She was standing pigeon toed, her knees bent inward and leaning awkwardly on him before he picked her up like a new bride, making sure the blanket was closed at her legs, and began to walk out of the room. "Doc! I weigh too much, you'll hurt yourself!" Came her instinctual reply which made him furrow his brows a bit.

"I'm not sure if you know this," He began, his accent almost accentuating his voice as he spoke his piece. "But, when a person is starved for weeks on end, they tend to lose a bit of weight."

The hallways he began to carry her though we're lighted with shades of greens and oranges, a nearly steampunk, yet still futuristic feel to them as she looked ahead curiously.

_Wow, this building is HUGE! I wonder where we are. Back in Saudi Arabia? _

The doctor took a few turns, almost as if he was going in a complete circle, before he stopped at the entrance to a room with an already open, sliding door, making it seem as if it had no door to begin with. A walkway, large enough for several people to stand in a line, led to a platform in an otherwise floorless room. Upon the platform was an immense spiral staircase, Going up and down to underneath the platform, whilst another spiral, this time a larger one consisting of clothes racks circled around the stair, as if it were the only way to get to the clothing. Large curling columns that acted almost as cubbies for the metal racks to curl into, a honeycomb of twisting, rectangular sectors.

The racks disappeared back behind the columns before they could obstruct the walkway, giving a better view of the walls on the sides of it, which were curved. Small, white, circular, window-like objects adorned the walls, giving this room more of a white light than the hallways had, much like the normalcy of the hospital room she had just been in, once the lights had come up all the way.

Serenity's mouth fell agape, eyes as wide as tea saucers as she stared at the setting before her. She was set down on a small cushioned seat near one of the columns, the metal pole for a rack a few feet above her head. "Woah..." She murmured as she looked around the room in awe, allowing him to walk up to another column across the room, beaming at her impressed state.

"Neat, huh? Now, let's see, what do you prefer wearing? Skirts? Pants? Dresses? Shorts?" The man with sea glass eyes began to ramble as he pressed several buttons and the clothing began to move.

The soldier's eyes only grew wider as he began to offer clothing, the hangers moving down the racks and giving her only on possible thing to compare it with. "Oh, my God! This is like a closet based off Monster's Inc!" She nearly squealed, taking the Doctor aback a bit.

"What?"

"Monster's Inc! You know, that Pixar movie where the monsters have all the doors which are basically wormholes to another universe in which they are the inside of a child's closet?" The look she received prompted her to try and explain further. "The big blue guy with purple spots who was friends with the small green guy with one eye? They had to scare children to power their civilization?"

That definition seemed to ring a bell. "Sounds like somewhere I've been... but no, I've never seen it." Her brows furrowed at his response, about to make a comment, when he gestured to the clothing. "Well, what are you waiting for? Start lookin'!"

_Maybe if I stare at him, he'll remember that women have a teeny bit more clothing to put on than men do._

She gave him a look, almost as if she expected him to suddenly realize something. It took him a few moments before his shoulders slumped and he made a face. "Right. Hold on a mo'." He jumped the small rail onto the staircase and disappeared below the floor.

After a few minutes of audible rummaging he came back up with a small trunk and a pair of boxers that looked too small for him. "I've got nothing in that particular category for you to wear, so wear these for now and we'll look for something more suitable. Otherwise I don't know you're..." He gestured to her, obviously avoiding using the actual word for some reason. "Size. So, look through here and see if any of them fit. After that, just look around. If you like it, and it fits, it's yours." He smiled a bit and left her to browse, walking down into the floor once again, perhaps to look for something himself.

After finally re-teaching herself how to stand, and walk, she put on the boxers and found a black bra that was only a little too small, but was comfortable otherwise, lifting herself onto the ladder and beginning to look at the women's clothing in the wardrobe in front of her.

She couldn't explain the reason she trusted him enough to just leave the sheet on the bench, folded, as she climbed the staircase in boxers odie green boxers that reached her mid-thigh and a black bra, but she began to look for something suitable to wear.

After a little while she came out with some black, straight leg jeans, a deep blue button down blouse, and two different colored socks of green and purple.

_Hopefully my boots were salvageable..._

"Are you done?" the Doctor questioned, earning a shout of the affirmative from the soldier, who met him on the platform once again. He had changed his shirt, from a color she couldn't quite remember, to a light grey, seeming like an almost jersey fabric. "Well, look at you. You look as good as new, Lieutenant."

"Please, Doc, call me Serenity... or something. I don't think I've actually felt like a soldier since I started losing hope." She finished the sentence solemnly, but laughed softly afterwards, trying to lift the mood.

"S.R then."

"Why S.R?"

"Why do you keep calling me Doc?"

"It's a nickname I- Gotcha." She chuckled as she understood, the letters having no other significance than being her initials. "So where are we, Doc?"

Suddenly a great lurch was felt, jarring her into him so that she was on his chest when he fell on his back. The Doctor's head popped off the floor and he spoke before she could get her breath back, eyes wide with excitement. "Well, I guess we need to find out, don't we?"


End file.
